AMBER Archive (2006)

Subject: AMBER: analysis of ATOMs in ´certain range distance during simulation

From: pkb bioinfo (pkstruct_at_gmail.com)
Date: Wed Jul 05 2006 - 22:37:46 CDT

 Dear Amber users,

I am a new AMBER user and finding it very difficult to analyse my simulation
result.
I need to know atoms in a range (4A) of a certain residue of importance
during
simulation.Actually I want to know which residues or atoms come close to my
docked
substate during course of simulation.

I saw in the carnal it was possible but carnal module is not present in
AMBER8.
In ptraj hbond analysis it will give only potential hydrogen bonds.
So anyone please help me in this regard.

best regards
Pravas

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